The simple fix described in this email:

http://www.nabble.com/mouse-yank-at-point-in-Comint-modes-td7731895.html

never got applied to the trunk.  Thus the problem of yanks not honoring
mouse-yank-at-point is still present in comint mode.  Is it possible that it
could be applied?  Here is an updated version of the patch:

--- emacs/lisp/comint.el    2008-09-08 14:46:43.000000000 -0600
+++ emacs-080908/lisp/comint.el    2008-09-11 15:24:11.000000000 -0600
@@ -815,7 +815,7 @@
 If there is no previous input at point, run the command specified
 by the global keymap (usually `mouse-yank-at-point')."
   (interactive "e")
-  (mouse-set-point event)
+  (unless mouse-yank-at-point (mouse-set-point event))
   (let ((pos (posn-point (event-end event)))
     field input)
     (with-selected-window (posn-window (event-end event))

Thanks,
Bob